diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index be14a237e5..9b8c7febf4 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -6,6 +6,8 @@ dump image command dump movie command ================== +(see below for :ref:`dump_modify options ` specific to dump image/movie) + Syntax """""" @@ -15,7 +17,7 @@ Syntax * ID = user-assigned name for the dump * group-ID = ID of the group of atoms to be imaged -* style = *image* or *movie* = style of dump command (other styles *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump ` doc page) +* style = *image* or *movie* = style of dump command (other styles such as *atom* or *cfg* or *dcd* or *xtc* or *xyz* or *local* or *custom* are discussed on the :doc:`dump ` doc page) * N = dump every this many timesteps * file = name of file to write image to * color = atom attribute that determines color of each atom @@ -79,6 +81,69 @@ Syntax seed = random # seed (positive integer) dfactor = strength of shading from 0.0 to 1.0 + +.. _dump_modify_image: + +dump_modify options for dump image/movie +======================================== + +Syntax +"""""" + +.. parsed-literal:: + + dump_modify dump-ID keyword values ... + +* these keywords apply only to the *image* and *movie* styles and are documented on this page +* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* +* see the :doc:`dump modify ` doc page for more general keywords + + .. parsed-literal:: + + *acolor* args = type color + type = atom type or range of types (see below) + color = name of color or color1/color2/... + *adiam* args = type diam + type = atom type or range of types (see below) + diam = diameter of atoms of that type (distance units) + *amap* args = lo hi style delta N entry1 entry2 ... entryN + lo = number or *min* = lower bound of range of color map + hi = number or *max* = upper bound of range of color map + style = 2 letters = "c" or "d" or "s" plus "a" or "f" + "c" for continuous + "d" for discrete + "s" for sequential + "a" for absolute + "f" for fractional + delta = binsize (only used for style "s", otherwise ignored) + binsize = range is divided into bins of this width + N = # of subsequent entries + entry = value color (for continuous style) + value = number or *min* or *max* = single value within range + color = name of color used for that value + entry = lo hi color (for discrete style) + lo/hi = number or *min* or *max* = lower/upper bound of subset of range + color = name of color used for that subset of values + entry = color (for sequential style) + color = name of color used for a bin of values + *backcolor* arg = color + color = name of color for background + *bcolor* args = type color + type = bond type or range of types (see below) + color = name of color or color1/color2/... + *bdiam* args = type diam + type = bond type or range of types (see below) + diam = diameter of bonds of that type (distance units) + *boxcolor* arg = color + color = name of color for simulation box lines and processor sub-domain lines + *color* args = name R G B + name = name of color + R,G,B = red/green/blue numeric values from 0.0 to 1.0 + *bitrate* arg = rate + rate = target bitrate for movie in kbps + *framerate* arg = fps + fps = frames per second for movie + Examples """""""" @@ -91,6 +156,8 @@ Examples dump m1 all movie 1000 movie.avi type type size 640 480 dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720 + dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red + Description """"""""""" @@ -145,10 +212,10 @@ is used. Similarly, the format of the resulting movie is chosen with the *movie* dump style. This is handled by the underlying FFmpeg converter and thus details have to be looked up in the `FFmpeg documentation -`_. -Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif -Additional settings of the movie compression like bitrate and -framerate can be set using the :doc:`dump_modify ` command. +`_. Typical examples are: .avi, .mpg, +.m4v, .mp4, .mkv, .flv, .mov, .gif Additional settings of the movie +compression like bitrate and framerate can be set using the +dump_modify command as described below. To write out JPEG and PNG format files, you must build LAMMPS with support for the corresponding JPEG or PNG library. To convert images @@ -210,19 +277,20 @@ to colors is as follows: * type 6 = cyan and repeats itself for types > 6. This mapping can be changed by the -:doc:`dump_modify acolor ` command. +"dump_modify acolor" command, as described below. If *type* is specified for the *diameter* setting then the diameter of each atom is determined by its atom type. By default all types have -diameter 1.0. This mapping can be changed by the :doc:`dump_modify adiam ` command. +diameter 1.0. This mapping can be changed by the "dump_modify adiam" +command, as described below. If *element* is specified for the *color* and/or *diameter* setting, then the color and/or diameter of each atom is determined by which element it is, which in turn is specified by the element-to-type -mapping specified by the "dump_modify element" command. By default -every atom type is C (carbon). Every element has a color and diameter -associated with it, which is the same as the colors and sizes used by -the `AtomEye `_ visualization package. +mapping specified by the "dump_modify element" command, as described +below. By default every atom type is C (carbon). Every element has a +color and diameter associated with it, which is the same as the colors +and sizes used by the `AtomEye `_ visualization package. .. _atomeye: http://li.mit.edu/Archive/Graphics/A/ @@ -232,13 +300,13 @@ settings, they are interpreted in the following way. If "vx", for example, is used as the *color* setting, then the color of the atom will depend on the x-component of its velocity. The association of a per-atom value with a specific color is determined by -a "color map", which can be specified via the -:doc:`dump_modify ` command. The basic idea is that the -atom-attribute will be within a range of values, and every value -within the range is mapped to a specific color. Depending on how the -color map is defined, that mapping can take place via interpolation so -that a value of -3.2 is halfway between "red" and "blue", or -discretely so that the value of -3.2 is "orange". +a "color map", which can be specified via the dump_modify command, as +described below. The basic idea is that the atom-attribute will be +within a range of values, and every value within the range is mapped +to a specific color. Depending on how the color map is defined, that +mapping can take place via interpolation so that a value of -3.2 is +halfway between "red" and "blue", or discretely so that the value of +-3.2 is "orange". If "vx", for example, is used as the *diameter* setting, then the atom will be rendered using the x-component of its velocity as the @@ -251,9 +319,10 @@ diameter, which can be used as the *diameter* setting. The various keywords listed above control how the image is rendered. As listed below, all of the keywords have defaults, most of which you -will likely not need to change. The :doc:`dump modify ` -also has options specific to the dump image style, particularly for -assigning colors to atoms, bonds, and other image features. +will likely not need to change. As described below, the dump modify +command also has options specific to the dump image style, +particularly for assigning colors to atoms, bonds, and other image +features. ---------- @@ -295,7 +364,7 @@ types to colors is as follows: * type 6 = cyan and repeats itself for bond types > 6. This mapping can be changed by -the :doc:`dump_modify bcolor ` command. +the "dump_modify bcolor" command, as described below. The bond *width* value can be a numeric value or *atom* or *type* (or *none* as indicated above). @@ -310,7 +379,8 @@ of the 2 atoms in the bond. If *type* is specified for the *width* value then the diameter of each bond is determined by its bond type. By default all types have -diameter 0.5. This mapping can be changed by the :doc:`dump_modify bdiam ` command. +diameter 0.5. This mapping can be changed by the "dump_modify bdiam" command, +as described below. ---------- @@ -330,7 +400,7 @@ mapping of types to colors is as follows: * type 6 = cyan and repeats itself for types > 6. There is not yet an option to -change this via the :doc:`dump_modify ` command. +change this via the dump_modify command. The line *width* can only be a numeric value, which specifies that all lines will be drawn as cylinders with that diameter, e.g. 1.0, which @@ -357,7 +427,7 @@ default the mapping of types to colors is as follows: * type 6 = cyan and repeats itself for types > 6. There is not yet an option to -change this via the :doc:`dump_modify ` command. +change this via the dump_modify command. ---------- @@ -390,7 +460,7 @@ particle. By default the mapping of types to colors is as follows: * type 6 = cyan and repeats itself for types > 6. There is not yet an option to -change this via the :doc:`dump_modify ` command. +change this via the dump_modify command. ---------- @@ -414,7 +484,7 @@ the mapping of types to colors is as follows: * type 6 = cyan and repeats itself for types > 6. There is not yet an option to -change this via the :doc:`dump_modify ` command. +change this via the dump_modify command. ---------- @@ -488,7 +558,8 @@ are rendered as thin cylinders in the image. If *no* is set, then the box boundaries are not drawn and the *diam* setting is ignored. If *yes* is set, the 12 edges of the box are drawn, with a diameter that is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for -2d). The color of the box boundaries can be set with the :doc:`dump_modify boxcolor ` command. +2d). The color of the box boundaries can be set with the "dump_modify +boxcolor" command. The *axes* keyword determines if and how the coordinate axes are rendered as thin cylinders in the image. If *no* is set, then the @@ -507,7 +578,8 @@ set (default), then the sub-domain boundaries are not drawn and the *diam* setting is ignored. If *yes* is set, the 12 edges of each processor sub-domain are drawn, with a diameter that is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color -of the sub-domain boundaries can be set with the :doc:`dump_modify boxcolor ` command. +of the sub-domain boundaries can be set with the "dump_modify +boxcolor" command. ---------- @@ -607,9 +679,272 @@ Play the movie: ---------- -See the :doc:`Modify ` page for information on how to add -new compute and fix styles to LAMMPS to calculate per-atom quantities -which could then be output into dump files. +Dump_modify keywords for dump image and dump movie +"""""""""""""""""""""""""""""""""""""""""""""""""" + +The following dump_modify keywords apply only to the dump image and +dump movie styles. Any keyword that works with dump image also works +with dump movie, since the movie is simply a collection of images. +Some of the keywords only affect the dump movie style. The +descriptions give details. + +---------- + +The *acolor* keyword can be used with the dump image command, when its +atom color setting is *type*, to set the color that atoms of each type +will be drawn in the image. + +The specified *type* should be an integer from 1 to Ntypes = the +number of atom types. A wildcard asterisk can be used in place of or +in conjunction with the *type* argument to specify a range of atom +types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = +the number of atom types, then an asterisk with no numeric values +means all types from 1 to N. A leading asterisk means all types from +1 to n (inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n +(inclusive). + +The specified *color* can be a single color which is any of the 140 +pre-defined colors (see below) or a color name defined by the +"dump_modify color" command, as described below. Or it can be two or +more colors separated by a "/" character, e.g. red/green/blue. In the +former case, that color is assigned to all the specified atom types. +In the latter case, the list of colors are assigned in a round-robin +fashion to each of the specified atom types. + +---------- + +The *adiam* keyword can be used with the dump image command, when its +atom diameter setting is *type*, to set the size that atoms of each +type will be drawn in the image. The specified *type* should be an +integer from 1 to Ntypes. As with the *acolor* keyword, a wildcard +asterisk can be used as part of the *type* argument to specify a range +of atom types. The specified *diam* is the size in whatever distance +:doc:`units ` the input script is using, e.g. Angstroms. + +---------- + +The *amap* keyword can be used with the dump image command, with its +*atom* keyword, when its atom setting is an atom-attribute, to setup a +color map. The color map is used to assign a specific RGB +(red/green/blue) color value to an individual atom when it is drawn, +based on the atom's attribute, which is a numeric value, e.g. its +x-component of velocity if the atom-attribute "vx" was specified. + +The basic idea of a color map is that the atom-attribute will be +within a range of values, and that range is associated with a series +of colors (e.g. red, blue, green). An atom's specific value (vx = +-3.2) can then mapped to the series of colors (e.g. halfway between +red and blue), and a specific color is determined via an interpolation +procedure. + +There are many possible options for the color map, enabled by the +*amap* keyword. Here are the details. + +The *lo* and *hi* settings determine the range of values allowed for +the atom attribute. If numeric values are used for *lo* and/or *hi*, +then values that are lower/higher than that value are set to the +value. I.e. the range is static. If *lo* is specified as *min* or +*hi* as *max* then the range is dynamic, and the lower and/or +upper bound will be calculated each time an image is drawn, based +on the set of atoms being visualized. + +The *style* setting is two letters, such as "ca". The first letter is +either "c" for continuous, "d" for discrete, or "s" for sequential. +The second letter is either "a" for absolute, or "f" for fractional. + +A continuous color map is one in which the color changes continuously +from value to value within the range. A discrete color map is one in +which discrete colors are assigned to sub-ranges of values within the +range. A sequential color map is one in which discrete colors are +assigned to a sequence of sub-ranges of values covering the entire +range. + +An absolute color map is one in which the values to which colors are +assigned are specified explicitly as values within the range. A +fractional color map is one in which the values to which colors are +assigned are specified as a fractional portion of the range. For +example if the range is from -10.0 to 10.0, and the color red is to be +assigned to atoms with a value of 5.0, then for an absolute color map +the number 5.0 would be used. But for a fractional map, the number +0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0. + +The *delta* setting must be specified for all styles, but is only used +for the sequential style; otherwise the value is ignored. It +specifies the bin size to use within the range for assigning +consecutive colors to. For example, if the range is from -10.0 to +10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to +the range. The first will be from -10.0 <= color1 < -9.0, then second +from -9.0 <= color2 < -8.0, etc. + +The *N* setting is how many entries follow. The format of the entries +depends on whether the color map style is continuous, discrete or +sequential. In all cases the *color* setting can be any of the 140 +pre-defined colors (see below) or a color name defined by the +dump_modify color option. + +For continuous color maps, each entry has a *value* and a *color*\ . +The *value* is either a number within the range of values or *min* or +*max*\ . The *value* of the first entry must be *min* and the *value* +of the last entry must be *max*\ . Any entries in between must have +increasing values. Note that numeric values can be specified either +as absolute numbers or as fractions (0.0 to 1.0) of the range, +depending on the "a" or "f" in the style setting for the color map. + +Here is how the entries are used to determine the color of an +individual atom, given the value X of its atom attribute. X will fall +between 2 of the entry values. The color of the atom is linearly +interpolated (in each of the RGB values) between the 2 colors +associated with those entries. For example, if X = -5.0 and the 2 +surrounding entries are "red" at -10.0 and "blue" at 0.0, then the +atom's color will be halfway between "red" and "blue", which happens +to be "purple". + +For discrete color maps, each entry has a *lo* and *hi* value and a +*color*\ . The *lo* and *hi* settings are either numbers within the +range of values or *lo* can be *min* or *hi* can be *max*\ . The *lo* +and *hi* settings of the last entry must be *min* and *max*\ . Other +entries can have any *lo* and *hi* values and the sub-ranges of +different values can overlap. Note that numeric *lo* and *hi* values +can be specified either as absolute numbers or as fractions (0.0 to +1.0) of the range, depending on the "a" or "f" in the style setting +for the color map. + +Here is how the entries are used to determine the color of an +individual atom, given the value X of its atom attribute. The entries +are scanned from first to last. The first time that *lo* <= X <= +*hi*, X is assigned the color associated with that entry. You can +think of the last entry as assigning a default color (since it will +always be matched by X), and the earlier entries as colors that +override the default. Also note that no interpolation of a color RGB +is done. All atoms will be drawn with one of the colors in the list +of entries. + +For sequential color maps, each entry has only a *color*\ . Here is how +the entries are used to determine the color of an individual atom, +given the value X of its atom attribute. The range is partitioned +into N bins of width *binsize*\ . Thus X will fall in a specific bin +from 1 to N, say the Mth bin. If it falls on a boundary between 2 +bins, it is considered to be in the higher of the 2 bins. Each bin is +assigned a color from the E entries. If E < N, then the colors are +repeated. For example if 2 entries with colors red and green are +specified, then the odd numbered bins will be red and the even bins +green. The color of the atom is the color of its bin. Note that the +sequential color map is really a shorthand way of defining a discrete +color map without having to specify where all the bin boundaries are. + +Here is an example of using a sequential color map to color all the +atoms in individual molecules with a different color. See the +examples/pour/in.pour.2d.molecule input script for an example of how +this is used. + +.. code-block:: LAMMPS + + variable colors string & + "red green blue yellow white & + purple pink orange lime gray" + variable mol atom mol%10 + dump 1 all image 250 image.*.jpg v_mol type & + zoom 1.6 adiam 1.5 + dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors} + +In this case, 10 colors are defined, and molecule IDs are +mapped to one of the colors, even if there are 1000s of molecules. + +---------- + +The *backcolor* sets the background color of the images. The color +name can be any of the 140 pre-defined colors (see below) or a color +name defined by the dump_modify color option. + +---------- + +The *bcolor* keyword can be used with the dump image command, with its +*bond* keyword, when its color setting is *type*, to set the color +that bonds of each type will be drawn in the image. + +The specified *type* should be an integer from 1 to Nbondtypes = the +number of bond types. A wildcard asterisk can be used in place of or +in conjunction with the *type* argument to specify a range of bond +types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = +the number of bond types, then an asterisk with no numeric values +means all types from 1 to N. A leading asterisk means all types from +1 to n (inclusive). A trailing asterisk means all types from n to N +(inclusive). A middle asterisk means all types from m to n +(inclusive). + +The specified *color* can be a single color which is any of the 140 +pre-defined colors (see below) or a color name defined by the +dump_modify color option. Or it can be two or more colors separated +by a "/" character, e.g. red/green/blue. In the former case, that +color is assigned to all the specified bond types. In the latter +case, the list of colors are assigned in a round-robin fashion to each +of the specified bond types. + +---------- + +The *bdiam* keyword can be used with the dump image command, with its +*bond* keyword, when its diam setting is *type*, to set the diameter +that bonds of each type will be drawn in the image. The specified +*type* should be an integer from 1 to Nbondtypes. As with the +*bcolor* keyword, a wildcard asterisk can be used as part of the +*type* argument to specify a range of bond types. The specified +*diam* is the size in whatever distance :doc:`units ` you are +using, e.g. Angstroms. + +---------- + +The *bitrate* keyword can be used with the :doc:`dump movie +` command to define the size of the resulting movie file +and its quality via setting how many kbits per second are to be used +for the movie file. Higher bitrates require less compression and will +result in higher quality movies. The quality is also determined by +the compression format and encoder. The default setting is 2000 +kbit/s, which will result in average quality with older compression +formats. + +.. note:: + + Not all movie file formats supported by dump movie allow the + bitrate to be set. If not, the setting is silently ignored. + +---------- + +The *boxcolor* keyword sets the color of the simulation box drawn +around the atoms in each image as well as the color of processor +sub-domain boundaries. See the "dump image box" command for how to +specify that a box be drawn via the *box* keyword, and the sub-domain +boundaries via the *subbox* keyword. The color name can be any of the +140 pre-defined colors (see below) or a color name defined by the +dump_modify color option. + +---------- + +The *color* keyword allows definition of a new color name, in addition +to the 140-predefined colors (see below), and associates 3 +red/green/blue RGB values with that color name. The color name can +then be used with any other dump_modify keyword that takes a color +name as a value. The RGB values should each be floating point values +between 0.0 and 1.0 inclusive. + +When a color name is converted to RGB values, the user-defined color +names are searched first, then the 140 pre-defined color names. This +means you can also use the *color* keyword to overwrite one of the +pre-defined color names with new RBG values. + +---------- + +The *framerate* keyword can be used with the :doc:`dump movie +` command to define the duration of the resulting movie +file. Movie files written by the dump *movie* command have a default +frame rate of 24 frames per second and the images generated will be +converted at that rate. Thus a sequence of 1000 dump images will +result in a movie of about 42 seconds. To make a movie run longer you +can either generate images more frequently or lower the frame rate. +To speed a movie up, you can do the inverse. Using a frame rate +higher than 24 is not recommended, as it will result in simply +dropping the rendered images. It is more efficient to dump images less +frequently. ---------- @@ -664,7 +999,7 @@ Related commands Default """"""" -The defaults for the keywords are as follows: +The defaults for the dump image and dump movie keywords are as follows: * adiam = not specified (use diameter setting) * atom = yes @@ -682,3 +1017,101 @@ The defaults for the keywords are as follows: * subbox no 0.0 * shiny = 1.0 * ssao = no + +---------- + +The defaults for the dump_modify keywords specific to dump image and dump movie are as follows: + +* acolor = \* red/green/blue/yellow/aqua/cyan +* adiam = \* 1.0 +* amap = min max cf 0.0 2 min blue max red +* backcolor = black +* bcolor = \* red/green/blue/yellow/aqua/cyan +* bdiam = \* 0.5 +* bitrate = 2000 +* boxcolor = yellow +* color = 140 color names are pre-defined as listed below +* framerate = 24 + +---------- + +These are the standard 109 element names that LAMMPS pre-defines for +use with the dump image and dump_modify commands. + +* 1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne" +* 11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca" +* 21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn" +* 31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr" +* 41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn" +* 51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd" +* 61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb" +* 71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg" +* 81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th" +* 91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm" +* 101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt" + +---------- + +These are the 140 colors that LAMMPS pre-defines for use with the dump +image and dump_modify commands. Additional colors can be defined with +the dump_modify color command. The 3 numbers listed for each name are +the RGB (red/green/blue) values. Divide each value by 255 to get the +equivalent 0.0 to 1.0 value. + ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| aliceblue = 240, 248, 255 | antiquewhite = 250, 235, 215 | aqua = 0, 255, 255 | aquamarine = 127, 255, 212 | azure = 240, 255, 255 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| beige = 245, 245, 220 | bisque = 255, 228, 196 | black = 0, 0, 0 | blanchedalmond = 255, 255, 205 | blue = 0, 0, 255 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| blueviolet = 138, 43, 226 | brown = 165, 42, 42 | burlywood = 222, 184, 135 | cadetblue = 95, 158, 160 | chartreuse = 127, 255, 0 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| chocolate = 210, 105, 30 | coral = 255, 127, 80 | cornflowerblue = 100, 149, 237 | cornsilk = 255, 248, 220 | crimson = 220, 20, 60 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| cyan = 0, 255, 255 | darkblue = 0, 0, 139 | darkcyan = 0, 139, 139 | darkgoldenrod = 184, 134, 11 | darkgray = 169, 169, 169 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| darkgreen = 0, 100, 0 | darkkhaki = 189, 183, 107 | darkmagenta = 139, 0, 139 | darkolivegreen = 85, 107, 47 | darkorange = 255, 140, 0 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| darkorchid = 153, 50, 204 | darkred = 139, 0, 0 | darksalmon = 233, 150, 122 | darkseagreen = 143, 188, 143 | darkslateblue = 72, 61, 139 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| darkslategray = 47, 79, 79 | darkturquoise = 0, 206, 209 | darkviolet = 148, 0, 211 | deeppink = 255, 20, 147 | deepskyblue = 0, 191, 255 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| dimgray = 105, 105, 105 | dodgerblue = 30, 144, 255 | firebrick = 178, 34, 34 | floralwhite = 255, 250, 240 | forestgreen = 34, 139, 34 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| fuchsia = 255, 0, 255 | gainsboro = 220, 220, 220 | ghostwhite = 248, 248, 255 | gold = 255, 215, 0 | goldenrod = 218, 165, 32 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| gray = 128, 128, 128 | green = 0, 128, 0 | greenyellow = 173, 255, 47 | honeydew = 240, 255, 240 | hotpink = 255, 105, 180 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| indianred = 205, 92, 92 | indigo = 75, 0, 130 | ivory = 255, 240, 240 | khaki = 240, 230, 140 | lavender = 230, 230, 250 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| lavenderblush = 255, 240, 245 | lawngreen = 124, 252, 0 | lemonchiffon = 255, 250, 205 | lightblue = 173, 216, 230 | lightcoral = 240, 128, 128 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| lightcyan = 224, 255, 255 | lightgoldenrodyellow = 250, 250, 210 | lightgreen = 144, 238, 144 | lightgrey = 211, 211, 211 | lightpink = 255, 182, 193 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| lightsalmon = 255, 160, 122 | lightseagreen = 32, 178, 170 | lightskyblue = 135, 206, 250 | lightslategray = 119, 136, 153 | lightsteelblue = 176, 196, 222 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| lightyellow = 255, 255, 224 | lime = 0, 255, 0 | limegreen = 50, 205, 50 | linen = 250, 240, 230 | magenta = 255, 0, 255 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| maroon = 128, 0, 0 | mediumaquamarine = 102, 205, 170 | mediumblue = 0, 0, 205 | mediumorchid = 186, 85, 211 | mediumpurple = 147, 112, 219 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| mediumseagreen = 60, 179, 113 | mediumslateblue = 123, 104, 238 | mediumspringgreen = 0, 250, 154 | mediumturquoise = 72, 209, 204 | mediumvioletred = 199, 21, 133 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| midnightblue = 25, 25, 112 | mintcream = 245, 255, 250 | mistyrose = 255, 228, 225 | moccasin = 255, 228, 181 | navajowhite = 255, 222, 173 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| navy = 0, 0, 128 | oldlace = 253, 245, 230 | olive = 128, 128, 0 | olivedrab = 107, 142, 35 | orange = 255, 165, 0 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| orangered = 255, 69, 0 | orchid = 218, 112, 214 | palegoldenrod = 238, 232, 170 | palegreen = 152, 251, 152 | paleturquoise = 175, 238, 238 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| palevioletred = 219, 112, 147 | papayawhip = 255, 239, 213 | peachpuff = 255, 239, 213 | peru = 205, 133, 63 | pink = 255, 192, 203 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| plum = 221, 160, 221 | powderblue = 176, 224, 230 | purple = 128, 0, 128 | red = 255, 0, 0 | rosybrown = 188, 143, 143 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| royalblue = 65, 105, 225 | saddlebrown = 139, 69, 19 | salmon = 250, 128, 114 | sandybrown = 244, 164, 96 | seagreen = 46, 139, 87 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| seashell = 255, 245, 238 | sienna = 160, 82, 45 | silver = 192, 192, 192 | skyblue = 135, 206, 235 | slateblue = 106, 90, 205 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| slategray = 112, 128, 144 | snow = 255, 250, 250 | springgreen = 0, 255, 127 | steelblue = 70, 130, 180 | tan = 210, 180, 140 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| teal = 0, 128, 128 | thistle = 216, 191, 216 | tomato = 253, 99, 71 | turquoise = 64, 224, 208 | violet = 238, 130, 238 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ +| wheat = 245, 222, 179 | white = 255, 255, 255 | whitesmoke = 245, 245, 245 | yellow = 255, 255, 0 | yellowgreen = 154, 205, 50 | ++-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 5fea976e70..33f7141762 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -3,6 +3,9 @@ dump_modify command =================== +:doc:`dump_modify ` command for image/movie options +=============================================================== + Syntax """""" @@ -12,8 +15,9 @@ Syntax * dump-ID = ID of dump to modify * one or more keyword/value pairs may be appended + * these keywords apply to various dump styles -* keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *fileper* or *first* or *flush* or *format* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap* +* keyword = *append* or *at* or *buffer* or *delay* or *element* or *every* or *fileper* or *first* or *flush* or *format* or *header* or *image* or *label* or *maxfiles* or *nfile* or *pad* or *pbc* or *precision* or *region* or *refresh* or *scale* or *sfactor* or *sort* or *tfactor* or *thermo* or *thresh* or *time* or *units* or *unwrap* .. parsed-literal:: @@ -35,6 +39,9 @@ Syntax *format* args = *line* string, *int* string, *float* string, M string, or *none* string = C-style format string M = integer from 1 to N, where N = # of per-atom quantities being output + *header* arg = *yes* or *no* + *yes* to write the header + *no* to not write the header *image* arg = *yes* or *no* *label* arg = string string = character string (e.g. BONDS) to use in header of dump local file @@ -66,56 +73,11 @@ Syntax *unwrap* arg = *yes* or *no* * these keywords apply only to the *image* and *movie* :doc:`styles ` -* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* or *header* +* keyword = *acolor* or *adiam* or *amap* or *backcolor* or *bcolor* or *bdiam* or *boxcolor* or *color* or *bitrate* or *framerate* .. parsed-literal:: - *acolor* args = type color - type = atom type or range of types (see below) - color = name of color or color1/color2/... - *adiam* args = type diam - type = atom type or range of types (see below) - diam = diameter of atoms of that type (distance units) - *amap* args = lo hi style delta N entry1 entry2 ... entryN - lo = number or *min* = lower bound of range of color map - hi = number or *max* = upper bound of range of color map - style = 2 letters = "c" or "d" or "s" plus "a" or "f" - "c" for continuous - "d" for discrete - "s" for sequential - "a" for absolute - "f" for fractional - delta = binsize (only used for style "s", otherwise ignored) - binsize = range is divided into bins of this width - N = # of subsequent entries - entry = value color (for continuous style) - value = number or *min* or *max* = single value within range - color = name of color used for that value - entry = lo hi color (for discrete style) - lo/hi = number or *min* or *max* = lower/upper bound of subset of range - color = name of color used for that subset of values - entry = color (for sequential style) - color = name of color used for a bin of values - *backcolor* arg = color - color = name of color for background - *bcolor* args = type color - type = bond type or range of types (see below) - color = name of color or color1/color2/... - *bdiam* args = type diam - type = bond type or range of types (see below) - diam = diameter of bonds of that type (distance units) - *boxcolor* arg = color - color = name of color for simulation box lines and processor sub-domain lines - *color* args = name R G B - name = name of color - R,G,B = red/green/blue numeric values from 0.0 to 1.0 - *bitrate* arg = rate - rate = target bitrate for movie in kbps - *framerate* arg = fps - fps = frames per second for movie - *header* arg = *yes* or *no* - *yes* to write the header - *no* to not write the header + see the :doc:`dump image ` doc page for details * these keywords apply only to the */gz* and */zstd* dump styles * keyword = *compression_level* @@ -126,7 +88,7 @@ Syntax level = integer specifying the compression level that should be used (see below for supported levels) * these keywords apply only to the */zstd* dump styles -* keyword = *compression_level* +* keyword = *checksum* .. parsed-literal:: @@ -144,7 +106,6 @@ Examples dump_modify xtcdump precision 10000 sfactor 0.1 dump_modify 1 every 1000 nfile 20 dump_modify 1 every v_myVar - dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red Description """"""""""" @@ -163,8 +124,9 @@ which allow for use of MPI-IO. ---------- -These keywords apply to various dump styles, including the :doc:`dump image ` and :doc:`dump movie ` styles. The -description gives details. +Unless otherwise noted, the following keywords apply to all the +various dump styles, including the :doc:`dump image ` and +:doc:`dump movie ` styles. ---------- @@ -380,6 +342,13 @@ The *fileper* keyword is documented below with the *nfile* keyword. ---------- +The *header* keyword toggles whether the dump file will include a header. +Excluding a header will reduce the size of the dump file for fixes such as +:doc:`fix pair/tracker ` which do not require the information +typically written to the header. + +---------- + The *image* keyword applies only to the dump *atom* style. If the image value is *yes*, 3 flags are appended to each atom's coords which are the absolute box image of the atom in each dimension. For @@ -715,297 +684,27 @@ box size stored with the snapshot. ---------- -These keywords apply only to the :doc:`dump image ` and -:doc:`dump movie ` styles. Any keyword that affects an -image, also affects a movie, since the movie is simply a collection of -images. Some of the keywords only affect the :doc:`dump movie ` style. The descriptions give details. +The COMPRESS package offers both GZ and Zstd compression variants of +styles atom, custom, local, cfg, and xyz. When using these styles the +compression level can be controlled by the :code:`compression_level` +keyword. File names with these styles have to end in either +:code:`.gz` or :code:`.zst`. ----------- - -The *acolor* keyword can be used with the :doc:`dump image ` -command, when its atom color setting is *type*, to set the color that -atoms of each type will be drawn in the image. - -The specified *type* should be an integer from 1 to Ntypes = the -number of atom types. A wildcard asterisk can be used in place of or -in conjunction with the *type* argument to specify a range of atom -types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the -number of atom types, then an asterisk with no numeric values means -all types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). - -The specified *color* can be a single color which is any of the 140 -pre-defined colors (see below) or a color name defined by the -dump_modify color option. Or it can be two or more colors separated -by a "/" character, e.g. red/green/blue. In the former case, that -color is assigned to all the specified atom types. In the latter -case, the list of colors are assigned in a round-robin fashion to each -of the specified atom types. - ----------- - -The *adiam* keyword can be used with the :doc:`dump image ` -command, when its atom diameter setting is *type*, to set the size -that atoms of each type will be drawn in the image. The specified -*type* should be an integer from 1 to Ntypes. As with the *acolor* -keyword, a wildcard asterisk can be used as part of the *type* -argument to specify a range of atom types. The specified *diam* is -the size in whatever distance :doc:`units ` the input script is -using, e.g. Angstroms. - ----------- - -The *amap* keyword can be used with the :doc:`dump image ` -command, with its *atom* keyword, when its atom setting is an -atom-attribute, to setup a color map. The color map is used to assign -a specific RGB (red/green/blue) color value to an individual atom when -it is drawn, based on the atom's attribute, which is a numeric value, -e.g. its x-component of velocity if the atom-attribute "vx" was -specified. - -The basic idea of a color map is that the atom-attribute will be -within a range of values, and that range is associated with a series -of colors (e.g. red, blue, green). An atom's specific value (vx = --3.2) can then mapped to the series of colors (e.g. halfway between -red and blue), and a specific color is determined via an interpolation -procedure. - -There are many possible options for the color map, enabled by the -*amap* keyword. Here are the details. - -The *lo* and *hi* settings determine the range of values allowed for -the atom attribute. If numeric values are used for *lo* and/or *hi*, -then values that are lower/higher than that value are set to the -value. I.e. the range is static. If *lo* is specified as *min* or -*hi* as *max* then the range is dynamic, and the lower and/or -upper bound will be calculated each time an image is drawn, based -on the set of atoms being visualized. - -The *style* setting is two letters, such as "ca". The first letter is -either "c" for continuous, "d" for discrete, or "s" for sequential. -The second letter is either "a" for absolute, or "f" for fractional. - -A continuous color map is one in which the color changes continuously -from value to value within the range. A discrete color map is one in -which discrete colors are assigned to sub-ranges of values within the -range. A sequential color map is one in which discrete colors are -assigned to a sequence of sub-ranges of values covering the entire -range. - -An absolute color map is one in which the values to which colors are -assigned are specified explicitly as values within the range. A -fractional color map is one in which the values to which colors are -assigned are specified as a fractional portion of the range. For -example if the range is from -10.0 to 10.0, and the color red is to be -assigned to atoms with a value of 5.0, then for an absolute color map -the number 5.0 would be used. But for a fractional map, the number -0.75 would be used since 5.0 is 3/4 of the way from -10.0 to 10.0. - -The *delta* setting must be specified for all styles, but is only used -for the sequential style; otherwise the value is ignored. It -specifies the bin size to use within the range for assigning -consecutive colors to. For example, if the range is from -10.0 to -10.0 and a *delta* of 1.0 is used, then 20 colors will be assigned to -the range. The first will be from -10.0 <= color1 < -9.0, then second -from -9.0 <= color2 < -8.0, etc. - -The *N* setting is how many entries follow. The format of the entries -depends on whether the color map style is continuous, discrete or -sequential. In all cases the *color* setting can be any of the 140 -pre-defined colors (see below) or a color name defined by the -dump_modify color option. - -For continuous color maps, each entry has a *value* and a *color*\ . -The *value* is either a number within the range of values or *min* or -*max*\ . The *value* of the first entry must be *min* and the *value* -of the last entry must be *max*\ . Any entries in between must have -increasing values. Note that numeric values can be specified either -as absolute numbers or as fractions (0.0 to 1.0) of the range, -depending on the "a" or "f" in the style setting for the color map. - -Here is how the entries are used to determine the color of an -individual atom, given the value X of its atom attribute. X will fall -between 2 of the entry values. The color of the atom is linearly -interpolated (in each of the RGB values) between the 2 colors -associated with those entries. For example, if X = -5.0 and the 2 -surrounding entries are "red" at -10.0 and "blue" at 0.0, then the -atom's color will be halfway between "red" and "blue", which happens -to be "purple". - -For discrete color maps, each entry has a *lo* and *hi* value and a -*color*\ . The *lo* and *hi* settings are either numbers within the -range of values or *lo* can be *min* or *hi* can be *max*\ . The *lo* -and *hi* settings of the last entry must be *min* and *max*\ . Other -entries can have any *lo* and *hi* values and the sub-ranges of -different values can overlap. Note that numeric *lo* and *hi* values -can be specified either as absolute numbers or as fractions (0.0 to -1.0) of the range, depending on the "a" or "f" in the style setting -for the color map. - -Here is how the entries are used to determine the color of an -individual atom, given the value X of its atom attribute. The entries -are scanned from first to last. The first time that *lo* <= X <= -*hi*, X is assigned the color associated with that entry. You can -think of the last entry as assigning a default color (since it will -always be matched by X), and the earlier entries as colors that -override the default. Also note that no interpolation of a color RGB -is done. All atoms will be drawn with one of the colors in the list -of entries. - -For sequential color maps, each entry has only a *color*\ . Here is how -the entries are used to determine the color of an individual atom, -given the value X of its atom attribute. The range is partitioned -into N bins of width *binsize*\ . Thus X will fall in a specific bin -from 1 to N, say the Mth bin. If it falls on a boundary between 2 -bins, it is considered to be in the higher of the 2 bins. Each bin is -assigned a color from the E entries. If E < N, then the colors are -repeated. For example if 2 entries with colors red and green are -specified, then the odd numbered bins will be red and the even bins -green. The color of the atom is the color of its bin. Note that the -sequential color map is really a shorthand way of defining a discrete -color map without having to specify where all the bin boundaries are. - -Here is an example of using a sequential color map to color all the -atoms in individual molecules with a different color. See the -examples/pour/in.pour.2d.molecule input script for an example of how -this is used. - -.. code-block:: LAMMPS - - variable colors string & - "red green blue yellow white & - purple pink orange lime gray" - variable mol atom mol%10 - dump 1 all image 250 image.*.jpg v_mol type & - zoom 1.6 adiam 1.5 - dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors} - -In this case, 10 colors are defined, and molecule IDs are -mapped to one of the colors, even if there are 1000s of molecules. - ----------- - -The *backcolor* sets the background color of the images. The color -name can be any of the 140 pre-defined colors (see below) or a color -name defined by the dump_modify color option. - ----------- - -The *bcolor* keyword can be used with the :doc:`dump image ` -command, with its *bond* keyword, when its color setting is *type*, to -set the color that bonds of each type will be drawn in the image. - -The specified *type* should be an integer from 1 to Nbondtypes = the -number of bond types. A wildcard asterisk can be used in place of or -in conjunction with the *type* argument to specify a range of bond -types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the -number of bond types, then an asterisk with no numeric values means -all types from 1 to N. A leading asterisk means all types from 1 to n -(inclusive). A trailing asterisk means all types from n to N -(inclusive). A middle asterisk means all types from m to n -(inclusive). - -The specified *color* can be a single color which is any of the 140 -pre-defined colors (see below) or a color name defined by the -dump_modify color option. Or it can be two or more colors separated -by a "/" character, e.g. red/green/blue. In the former case, that -color is assigned to all the specified bond types. In the latter -case, the list of colors are assigned in a round-robin fashion to each -of the specified bond types. - ----------- - -The *bdiam* keyword can be used with the :doc:`dump image ` -command, with its *bond* keyword, when its diam setting is *type*, to -set the diameter that bonds of each type will be drawn in the image. -The specified *type* should be an integer from 1 to Nbondtypes. As -with the *bcolor* keyword, a wildcard asterisk can be used as part of -the *type* argument to specify a range of bond types. The specified -*diam* is the size in whatever distance :doc:`units ` you are -using, e.g. Angstroms. - ----------- - -The *bitrate* keyword can be used with the :doc:`dump movie ` command to define the size of the resulting -movie file and its quality via setting how many kbits per second are -to be used for the movie file. Higher bitrates require less -compression and will result in higher quality movies. The quality is -also determined by the compression format and encoder. The default -setting is 2000 kbit/s, which will result in average quality with -older compression formats. - -.. note:: - - Not all movie file formats supported by dump movie allow the - bitrate to be set. If not, the setting is silently ignored. - ----------- - -The *boxcolor* keyword sets the color of the simulation box drawn -around the atoms in each image as well as the color of processor -sub-domain boundaries. See the "dump image box" command for how to -specify that a box be drawn via the *box* keyword, and the sub-domain -boundaries via the *subbox* keyword. The color name can be any of the -140 pre-defined colors (see below) or a color name defined by the -dump_modify color option. - ----------- - -The *color* keyword allows definition of a new color name, in addition -to the 140-predefined colors (see below), and associates 3 -red/green/blue RGB values with that color name. The color name can -then be used with any other dump_modify keyword that takes a color -name as a value. The RGB values should each be floating point values -between 0.0 and 1.0 inclusive. - -When a color name is converted to RGB values, the user-defined color -names are searched first, then the 140 pre-defined color names. This -means you can also use the *color* keyword to overwrite one of the -pre-defined color names with new RBG values. - ----------- - -The *framerate* keyword can be used with the :doc:`dump movie ` command to define the duration of the resulting -movie file. Movie files written by the dump *movie* command have a -default frame rate of 24 frames per second and the images generated -will be converted at that rate. Thus a sequence of 1000 dump images -will result in a movie of about 42 seconds. To make a movie run -longer you can either generate images more frequently or lower the -frame rate. To speed a movie up, you can do the inverse. Using a -frame rate higher than 24 is not recommended, as it will result in -simply dropping the rendered images. It is more efficient to dump -images less frequently. - ----------- - -The *header* keyword toggles whether the dump file will include a header. -Excluding a header will reduce the size of the dump file for fixes such as -:doc:`fix pair/tracker ` which do not require the information -typically written to the header. - ----------- - -The COMPRESS package offers both GZ and Zstd compression variants of styles -atom, custom, local, cfg, and xyz. When using these styles the compression -level can be controlled by the :code:`compression_level` parameter. File names -with these styles have to end in either :code:`.gz` or :code:`.zst`. - -GZ supports compression levels from -1 (default), 0 (no compression), and 1 to -9. 9 being the best compression. The COMPRESS :code:`/gz` styles use 9 as -default compression level. +GZ supports compression levels from -1 (default), 0 (no compression), +and 1 to +9. 9 being the best compression. The COMPRESS :code:`/gz` styles use 9 +as default compression level. Zstd offers a wider range of compression levels, including negative -levels that sacrifice compression for performance. 0 is the -default, positive levels are 1 to 22, with 22 being the most expensive +levels that sacrifice compression for performance. 0 is the default, +positive levels are 1 to 22, with 22 being the most expensive compression. Zstd promises higher compression/decompression speeds for similar compression ratios. For more details see `http://facebook.github.io/zstd/`. -In addition, Zstd compressed files can have a checksum of the entire -contents. The Zstd enabled dump styles enable this feature by default and it -can be disabled with the :code:`checksum` parameter. +In addition, Zstd compressed files can include a checksum of the +entire contents. The Zstd enabled dump styles enable this feature by +default and it can be disabled with the :code:`checksum` keyword. ---------- @@ -1046,100 +745,7 @@ The option defaults are * units = no * unwrap = no -* acolor = \* red/green/blue/yellow/aqua/cyan -* adiam = \* 1.0 -* amap = min max cf 0.0 2 min blue max red -* backcolor = black -* bcolor = \* red/green/blue/yellow/aqua/cyan -* bdiam = \* 0.5 -* bitrate = 2000 -* boxcolor = yellow -* color = 140 color names are pre-defined as listed below -* framerate = 24 - * compression_level = 9 (gz variants) * compression_level = 0 (zstd variants) * checksum = yes (zstd variants) ----------- - -These are the standard 109 element names that LAMMPS pre-defines for -use with the :doc:`dump image ` and dump_modify commands. - -* 1-10 = "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne" -* 11-20 = "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca" -* 21-30 = "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn" -* 31-40 = "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr" -* 41-50 = "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn" -* 51-60 = "Sb", "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd" -* 61-70 = "Pm", "Sm", "Eu", "Gd", "Tb", "Dy", "Ho", "Er", "Tm", "Yb" -* 71-80 = "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", "Pt", "Au", "Hg" -* 81-90 = "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th" -* 91-100 = "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm" -* 101-109 = "Md", "No", "Lr", "Rf", "Db", "Sg", "Bh", "Hs", "Mt" - ----------- - -These are the 140 colors that LAMMPS pre-defines for use with the -:doc:`dump image ` and dump_modify commands. Additional -colors can be defined with the dump_modify color command. The 3 -numbers listed for each name are the RGB (red/green/blue) values. -Divide each value by 255 to get the equivalent 0.0 to 1.0 value. - -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| aliceblue = 240, 248, 255 | antiquewhite = 250, 235, 215 | aqua = 0, 255, 255 | aquamarine = 127, 255, 212 | azure = 240, 255, 255 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| beige = 245, 245, 220 | bisque = 255, 228, 196 | black = 0, 0, 0 | blanchedalmond = 255, 255, 205 | blue = 0, 0, 255 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| blueviolet = 138, 43, 226 | brown = 165, 42, 42 | burlywood = 222, 184, 135 | cadetblue = 95, 158, 160 | chartreuse = 127, 255, 0 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| chocolate = 210, 105, 30 | coral = 255, 127, 80 | cornflowerblue = 100, 149, 237 | cornsilk = 255, 248, 220 | crimson = 220, 20, 60 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| cyan = 0, 255, 255 | darkblue = 0, 0, 139 | darkcyan = 0, 139, 139 | darkgoldenrod = 184, 134, 11 | darkgray = 169, 169, 169 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| darkgreen = 0, 100, 0 | darkkhaki = 189, 183, 107 | darkmagenta = 139, 0, 139 | darkolivegreen = 85, 107, 47 | darkorange = 255, 140, 0 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| darkorchid = 153, 50, 204 | darkred = 139, 0, 0 | darksalmon = 233, 150, 122 | darkseagreen = 143, 188, 143 | darkslateblue = 72, 61, 139 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| darkslategray = 47, 79, 79 | darkturquoise = 0, 206, 209 | darkviolet = 148, 0, 211 | deeppink = 255, 20, 147 | deepskyblue = 0, 191, 255 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| dimgray = 105, 105, 105 | dodgerblue = 30, 144, 255 | firebrick = 178, 34, 34 | floralwhite = 255, 250, 240 | forestgreen = 34, 139, 34 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| fuchsia = 255, 0, 255 | gainsboro = 220, 220, 220 | ghostwhite = 248, 248, 255 | gold = 255, 215, 0 | goldenrod = 218, 165, 32 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| gray = 128, 128, 128 | green = 0, 128, 0 | greenyellow = 173, 255, 47 | honeydew = 240, 255, 240 | hotpink = 255, 105, 180 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| indianred = 205, 92, 92 | indigo = 75, 0, 130 | ivory = 255, 240, 240 | khaki = 240, 230, 140 | lavender = 230, 230, 250 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| lavenderblush = 255, 240, 245 | lawngreen = 124, 252, 0 | lemonchiffon = 255, 250, 205 | lightblue = 173, 216, 230 | lightcoral = 240, 128, 128 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| lightcyan = 224, 255, 255 | lightgoldenrodyellow = 250, 250, 210 | lightgreen = 144, 238, 144 | lightgrey = 211, 211, 211 | lightpink = 255, 182, 193 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| lightsalmon = 255, 160, 122 | lightseagreen = 32, 178, 170 | lightskyblue = 135, 206, 250 | lightslategray = 119, 136, 153 | lightsteelblue = 176, 196, 222 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| lightyellow = 255, 255, 224 | lime = 0, 255, 0 | limegreen = 50, 205, 50 | linen = 250, 240, 230 | magenta = 255, 0, 255 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| maroon = 128, 0, 0 | mediumaquamarine = 102, 205, 170 | mediumblue = 0, 0, 205 | mediumorchid = 186, 85, 211 | mediumpurple = 147, 112, 219 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| mediumseagreen = 60, 179, 113 | mediumslateblue = 123, 104, 238 | mediumspringgreen = 0, 250, 154 | mediumturquoise = 72, 209, 204 | mediumvioletred = 199, 21, 133 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| midnightblue = 25, 25, 112 | mintcream = 245, 255, 250 | mistyrose = 255, 228, 225 | moccasin = 255, 228, 181 | navajowhite = 255, 222, 173 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| navy = 0, 0, 128 | oldlace = 253, 245, 230 | olive = 128, 128, 0 | olivedrab = 107, 142, 35 | orange = 255, 165, 0 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| orangered = 255, 69, 0 | orchid = 218, 112, 214 | palegoldenrod = 238, 232, 170 | palegreen = 152, 251, 152 | paleturquoise = 175, 238, 238 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| palevioletred = 219, 112, 147 | papayawhip = 255, 239, 213 | peachpuff = 255, 239, 213 | peru = 205, 133, 63 | pink = 255, 192, 203 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| plum = 221, 160, 221 | powderblue = 176, 224, 230 | purple = 128, 0, 128 | red = 255, 0, 0 | rosybrown = 188, 143, 143 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| royalblue = 65, 105, 225 | saddlebrown = 139, 69, 19 | salmon = 250, 128, 114 | sandybrown = 244, 164, 96 | seagreen = 46, 139, 87 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| seashell = 255, 245, 238 | sienna = 160, 82, 45 | silver = 192, 192, 192 | skyblue = 135, 206, 235 | slateblue = 106, 90, 205 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| slategray = 112, 128, 144 | snow = 255, 250, 250 | springgreen = 0, 255, 127 | steelblue = 70, 130, 180 | tan = 210, 180, 140 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| teal = 0, 128, 128 | thistle = 216, 191, 216 | tomato = 253, 99, 71 | turquoise = 64, 224, 208 | violet = 238, 130, 238 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+ -| wheat = 245, 222, 179 | white = 255, 255, 255 | whitesmoke = 245, 245, 245 | yellow = 255, 255, 0 | yellowgreen = 154, 205, 50 | -+-------------------------------+--------------------------------------+---------------------------------+--------------------------------+--------------------------------+